{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Yousefi R"],"funding":["National Institute of General Medical Sciences","NIGMS NIH HHS","Cancer Prevention and Research Institute of Texas","National Science Foundation"],"pagination":["104110"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8439718"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["155(10)"],"pubmed_abstract":["The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein "],"journal":["The Journal of chemical physics"],"pubmed_title":["Contributions of higher-order proximal distribution functions to solvent structure around proteins."],"pmcid":["PMC8439718"],"funding_grant_id":["CHE-1709310","RP170593","GM037657","R01 GM037657"],"pubmed_authors":["Yousefi R","Pettitt BM","Lynch GC","Galbraith M"],"additional_accession":[]},"is_claimable":false,"name":"Contributions of higher-order proximal distribution functions to solvent structure around proteins.","description":"The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein ","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Sep","modification":"2025-04-26T07:18:16.972Z","creation":"2025-04-06T12:12:48.349Z"},"accession":"S-EPMC8439718","cross_references":{"pubmed":["34525817"],"doi":["10.1063/5.0062580"]}}